ArticleNucleic acids research2020
HydraPsiSeq: a method for systematic and quantitative mapping of pseudouridines in RNA.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers, 1 of them a synthesis that pooled it.
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Who cites it
94 citing papers in PubMed, 1 synthesis or guideline pooled it, 150 citations in OpenAlex.
- Current Practice in Bicistronic IRES Reporter Use: A Systematic Review.International journal of molecular sciences · 2021Pooled it
- Updated guide to RNA quantification by RNA sequencing and reverse transcription-qPCR.Molecules and cells · 2026Article
- SNHG family lncRNAs promote Ewing sarcoma cell fitness through intronic snoRNA-guided rRNA modifications.NAR cancer · 2026Article
- Ribosomal architecture and rRNA modification landscape in the tick-borne parasite Babesia divergens.Nature communications · 2026Article
- Comprehensive post-transcriptional modification profiles in individual Staphylococcus aureus tRNA species.Nucleic acids research · 2026Article
- Evaluation of Dorado v5.2.0 de novo basecalling models for the detection of tRNA modifications using RNA004 chemistry.BMC genomics · 2026Article
- Ψ-Atlas: An Integrated Atlas for Pseudouridine Epitranscriptome.Genomics, proteomics & bioinformatics · 2026Article
- Trub1-mediated pseudouridylation is dispensable for immune cell development and homeostasis.Genes and immunity · 2026Article
- Review
- Ribosome heterogeneity and specialization in musculoskeletal physiology and pathology.JBMR plus · 2026Article
- Structural analysis of uridine modifications in solved RNA structures.NAR genomics and bioinformatics · 2026Article
- Integrative analysis of nanopore direct RNA sequencing data reveals a global impact of pseudouridylation on mNPJ precision oncology · 2026Article
- Molecular Insights into Widespread Pseudouridine RNA Modifications: Implications for Women's Health and Disease.Biology · 2026Review
- Designing RNA sequencing experiments: A practical guide to reproducible gene expression analysis.Computational and structural biotechnology journal · 2026Review
- RNA modifications in cancer: from biological insights to therapeutic targets.Bioorganic & medicinal chemistry · 2026Review
- Advances in Quantitative Techniques for Mapping RNA Modifications.Life (Basel, Switzerland) · 2025Review
- Mechanistic insight into the pseudouridylation of RNA.RNA biology · 2025Review
- Computational limitations and future needs to unravel the full potential of 2'-O-methylation and C/D box snoRNAs.RNA biology · 2025Review
- Pseudouridine increases ribosome stability in a thermophilic eukaryote.Nucleic acids research · 2025Article
- Diverse expression and modification of tRNAs and tRNA-derived RNAs in 19 mouse tissues.bioRxiv : the preprint server for biology · 2025Article
34 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Developing methods for accurate detection of RNA modifications remains a major challenge in epitranscriptomics. Next-generation sequencing-based mapping approaches have recently emerged but, often, they are not quantitative and lack specificity. Pseudouridine (ψ), produced by uridine isomerization, is one of the most abundant RNA modification. ψ mapping classically involves derivatization with soluble carbodiimide (CMCT), which is prone to variation making this approach only semi-quantitative. Here, we developed 'HydraPsiSeq', a novel quantitative ψ mapping technique relying on specific protection from hydrazine/aniline cleavage. HydraPsiSeq is quantitative because the obtained signal directly reflects pseudouridine level. Furthermore, normalization to natural unmodified RNA and/or to synthetic in vitro transcripts allows absolute measurements of modification levels. HydraPsiSeq requires minute amounts of RNA (as low as 10-50 ng), making it compatible with high-throughput profiling of diverse biological and clinical samples. Exploring the potential of HydraPsiSeq, we profiled human rRNAs, revealing strong variations in pseudouridylation levels at ∼20-25 positions out of total 104 sites. We also observed the dynamics of rRNA pseudouridylation throughout chondrogenic differentiation of human bone marrow stem cells. In conclusion, HydraPsiSeq is a robust approach for the systematic mapping and accurate quantification of pseudouridines in RNAs with applications in disease, aging, development, differentiation and/or stress response.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.